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Assessment of fungal diversity in deep-sea sediments by multiple primer approach

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Abstract

Increasing evidence of the fungal diversity in deep-sea sediments has come from amplification of environmental DNA with fungal specific or eukaryote primer sets. In order to assess the fungal diversity in deep-sea sediments of the Central Indian Basin (CIB) at ~5,000 m depth, we amplified sediment DNA with four different primer sets. These were fungal-specific primer pair ITS1F/ITS4 (internal transcribed spacers), universal 18S rDNA primers NS1/NS2, Euk18S-42F/Euk18S-1492R and Euk18S-555F/Euk18S-1269R. One environmental library was constructed with each of the primer pairs, and 48 clones were sequenced per library. These sequences resulted in 8 fungal Operational Taxonomic Units (OTUs) with ITS and 19 OTUs with 18S rDNA primer sets respectively by taking into account the 2% sequence divergence cut-off for species delineation. These OTUs belonged to 20 distinct fungal genera of the phyla Ascomycota and Basidiomycota. Seven sequences were found to be divergent by 79–97% from the known sequences of the existing database and may be novel. A majority of the sequences clustered with known sequences of the existing taxa. The phylogenetic affiliation of a few fungal sequences with known environmental sequences from marine and hypersaline habitat suggests their autochthonous nature or adaptation to marine habitat. The amplification of sequences belonging to Exobasidiomycetes and Cystobasidiomycetes from deep-sea is being reported for the first time in this study. Amplification of fungal sequences with eukaryotic as well as fungal specific primers indicates that among eukaryotes, fungi appear to be a dominant group in the sampling site of the CIB.

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Acknowledgments

The first author is thankful to University Grants Commission for the award of Senior Research Fellowship and Dr. Rahul Sharma, NIO, Goa for the facilities extended during the research cruise. The crew members of the Russian research vessel Academic Borris Petrov are acknowledged for their support. The first two authors are grateful to the Director, NIO for the support extended. This is NIO’s contribution No. 5031.

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Authors and Affiliations

  1. Council for Scientific and Industrial Research, National Institute of Oceanography, Dona Paula, Goa, 403004, India

    Purnima Singh & Chandralata Raghukumar

  2. National Centre for Cell Sciences, Lab-III, Pune University Campus, Ganeshkhind, Pune, 411007, India

    Pankaj Verma & Yogesh Shouche

Authors
  1. Purnima Singh
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  2. Chandralata Raghukumar
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  3. Pankaj Verma
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  4. Yogesh Shouche
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Correspondence to Chandralata Raghukumar.

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Singh, P., Raghukumar, C., Verma, P. et al. Assessment of fungal diversity in deep-sea sediments by multiple primer approach. World J Microbiol Biotechnol 28, 659–667 (2012). https://doi.org/10.1007/s11274-011-0859-3

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  • DOI: https://doi.org/10.1007/s11274-011-0859-3

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